/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_DNA_TRANSLATION_H_
#define _U2_DNA_TRANSLATION_H_

#include <QStringList>

#include <U2Core/global.h>

namespace U2 {

class DNAAlphabet;

enum DNATranslationType {
    DNATranslationType_UNKNOWN,
    DNATranslationType_NUCL_2_NUCL,
    DNATranslationType_NUCL_2_COMPLNUCL,
    DNATranslationType_NUCL_2_AMINO,
    DNATranslationType_AMINO_2_AMINO,
    DNATranslationType_AMINO_2_NUCL,
    DNATranslationType_RAW_2_NUCL,
    DNATranslationType_RAW_2_AMINO
};

class U2CORE_EXPORT BaseDNATranslationIds : public QObject {
public:
    static const QString NUCL_DNA_DEFAULT_COMPLEMENT;
    static const QString NUCL_RNA_DEFAULT_COMPLEMENT;

    static const QString NUCL_DNA_EXTENDED_COMPLEMENT;
    static const QString NUCL_RNA_EXTENDED_COMPLEMENT;
};

#define DNATranslationID(n) "NCBI-GenBank #" #n
#define DNABackTranslationID(type, name) "BackTranslation/" #type "/" #name
#define AMINO_TT_GOBJECT_HINT "AminoTT"

class U2CORE_EXPORT DNATranslation {
public:
    DNATranslation(const QString &_id, const QString &_name, const DNAAlphabet *src, const DNAAlphabet *dst);
    virtual ~DNATranslation() {
    }

    virtual qint64 translate(const char *src, qint64 src_len, char *dst, qint64 dst_capacity) const = 0;
    virtual int translate(char *src_and_dst, int len) const = 0;

    const QString &getTranslationName() const {
        return name;
    }
    const QString &getTranslationId() const {
        return id;
    }

    DNATranslationType getDNATranslationType() const {
        return type;
    }

    const DNAAlphabet *getSrcAlphabet() const {
        return srcAlphabet;
    }

    const DNAAlphabet *getDstAlphabet() const {
        return dstAlphabet;
    }

    virtual bool isOne2One() const {
        return false;
    }

    virtual bool isThree2One() const {
        return false;
    }

    virtual bool isOne2Three() const {
        return false;
    }

    virtual QByteArray getOne2OneMapper() const {
        assert(0);
        return QByteArray(256, 0);
    }

    virtual char translate3to1(char c1, char c2, char c3) const {
        Q_UNUSED(c1);
        Q_UNUSED(c2);
        Q_UNUSED(c3);
        assert(0);
        return 0;
    }

    virtual char *translate1to3(char c) const {
        Q_UNUSED(c);
        assert(0);
        return NULL;
    }

protected:
    DNATranslationType type;
    QString name;
    QString id;
    const DNAAlphabet *srcAlphabet;
    const DNAAlphabet *dstAlphabet;
};

enum DNACodonGroup {
    DNACodonGroup_POLAR,
    DNACodonGroup_NONPOLAR,
    DNACodonGroup_BASIC,
    DNACodonGroup_ACIDIC,
    DNACodonGroup_STOP
};

class U2CORE_EXPORT DNACodon {
public:
    DNACodon(char s, QString code, QString name, DNACodonGroup gr)
        : symbol(s), threeLetterCode(code), fullName(name), group(gr) {
    }
    virtual ~DNACodon() {
    }
    void setLink(QString _link) {
        link = _link;
    }

    char getSymbol() const {
        return symbol;
    }
    QString getTreeLetterCode() const {
        return threeLetterCode;
    }
    QString getFullName() const {
        return fullName;
    }
    DNACodonGroup getCodonGroup() const {
        return group;
    }
    QString getLink() const {
        return link;
    }

private:
    char symbol;
    QString threeLetterCode;
    QString fullName;
    QString link;
    DNACodonGroup group;
};

class U2CORE_EXPORT DNATranslationRegistry : public QObject {
public:
    DNATranslationRegistry(QObject *p = 0)
        : QObject(p) {
    }
    ~DNATranslationRegistry();

    DNATranslation *getStandardGeneticCodeTranslation(const DNAAlphabet *srcAlphabet);

    QStringList getDNATranlations() const;

    QStringList getDNATranslationIds() const;

    QStringList getDNATranslationIds(const QString &name) const;

    void registerDNATranslation(DNATranslation *t);

    void registerDNACodon(DNACodon *codon);

    QList<DNATranslation *> lookupTranslation(const DNAAlphabet *srcAlphabet, DNATranslationType type);

    DNATranslation *lookupTranslation(const DNAAlphabet *srcAlphabet, DNATranslationType type, const QString &id);

    DNATranslation *lookupTranslation(const QString &id);

    DNATranslation *lookupTranslation(const DNAAlphabet *srcAlphabet, const QString &id);

    DNATranslation *lookupComplementTranslation(const DNAAlphabet *srcAlphabet);

    DNACodon *lookupCodon(char symbol);

private:
    QList<DNATranslation *> translations;
    QList<DNACodon *> codons;
};

}    // namespace U2

#endif
